diff TEisotools-1.1.a/TEiso/Bedtools_closest.py @ 13:feef9a0db09d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/TEiso/Bedtools_closest.py	Wed Jul 20 09:04:42 2016 -0400
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and,  more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+import os
+from commons.core.checker.CheckerUtils import CheckerUtils
+from commons.core.utils.RepetOptionParser import RepetOptionParser
+from commons.core.utils.FileUtils import FileUtils
+import subprocess
+
+class Bedtools_closest(object):
+         
+    def __init__(self, input_file_A = "", input_file_B = "", output_file = "", verbosity = 3):
+        self._input_file_A = input_file_A
+        self._input_file_B = input_file_B
+        self._output_file = output_file
+        self._verbosity = verbosity
+        
+    def setAttributesFromCmdLine(self):
+        description = "For each feature in A, finds the closest feature (upstream or downstream) in B.\n" 
+        usage = " Bedtools_closest [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf> -o <output_dir> \n"
+        parser = RepetOptionParser(description = description, usage = usage)
+        parser.add_option( '-a', '--input_file_A', dest='input_file_A', help='bed/gff/vcf' )
+        parser.add_option( '-b', '--input_file_B', dest='input_file_B', help='bed/gff/vcf' )
+        parser.add_option( '-o', '--output_file', dest='output_file', help='write all output in this file/bed/gff/vcf', default = "")
+        options, args = parser.parse_args()
+        self.setAttributesFromOptions(options)
+    
+    def setAttributesFromOptions(self, options):
+        self._input_file_A = options.input_file_A
+        self._input_file_B = options.input_file_B
+        self._output_file = options.output_file
+        
+    def checkExecutables(self):
+        if not CheckerUtils.isExecutableInUserPath("bedtools"):
+            raise Exception("ERROR: bedtools must be in your path")
+    
+    def checkOptions(self):   
+        if self._input_file_A != "":
+            if not FileUtils.isRessourceExists(self._input_file_A ):
+                raise Exception("ERROR: reference file %s does not exist!" % self._input_file_A )
+        else:
+            raise Exception("ERROR: No specified -a option!")
+        
+        if self._input_file_B != "":
+            if not FileUtils.isRessourceExists(self._input_file_B):
+                raise Exception("ERROR: reference file %s does not exist!" % self._input_file_B )
+        else:
+            raise Exception("ERROR: No specified -b option!")
+   
+    def getbedtoolsclosestCmd(self, file_A, file_B, output_file):
+        cmd = 'bedtools closest -a %s -b %s -d -D a > %s' % (file_A,file_B, output_file)
+        ##print cmd
+        return cmd
+    
+    def run(self):
+        self.checkExecutables()
+        self.checkOptions()
+        sortfileA = "%s.sorted" % self._input_file_A
+        sortfileB = "%s.sorted" % self._input_file_B
+        os.system("bedtools sort -i %s > %s " % (self._input_file_A, sortfileA))
+        os.system("bedtools sort -i %s > %s " % (self._input_file_B, sortfileB))
+
+        try:
+            if os.path.exists(self._output_file):
+                raise Exception("ERROR: %s already exists." % self._output_file)
+           
+            cmd_bedtoolsclosest = self.getbedtoolsclosestCmd(sortfileA, sortfileB, self._output_file)
+            ## hide output of subprocess: stdout = index_dir_stderr
+            fstdout = open( "bedtools_closest.log" , 'w' )
+            process = subprocess.Popen(cmd_bedtoolsclosest, shell = True, stdout = fstdout, stderr=subprocess.STDOUT)
+            returncode = process.wait()
+            fstdout.close()
+            # get stderr, allowing for case where it's very large
+            fstdout = open("bedtools_closest.log", 'rb' )
+            stderr = ''
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += fstdout.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                    pass
+            fstdout.close()
+            if returncode != 0:
+                    raise Exception, stderr
+            #os.system("mv cufflinks.log  %s/cufflinks.log " % workingDir)
+        except Exception:
+            raise Exception("ERROR in %s " % cmd_bedtoolsclosest)
+        
+                
+if __name__ == "__main__":
+    iLaunch = Bedtools_closest()
+    iLaunch.setAttributesFromCmdLine()
+    iLaunch.run()
+